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<html><head><title>Python: module src.inputgen</title>
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<td valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial">&nbsp;<br><big><big><strong><a href="src.html"><font color="#ffffff">src</font></a>.inputgen</strong></big></big> (21 April 2007)</font></td
><td align=right valign=bottom
><font color="#ffffff" face="helvetica, arial"><a href=".">index</a><br><a href="file:/Users/d3y382/workspaces/apbs/pdb2pqr/branches/pdb2pqr-1.7.1a/src/inputgen.py">/Users/d3y382/workspaces/apbs/pdb2pqr/branches/pdb2pqr-1.7.1a/src/inputgen.py</a></font></td></tr></table>
    <p><tt>inputgen&nbsp;class<br>
&nbsp;<br>
Create&nbsp;an&nbsp;APBS&nbsp;input&nbsp;file&nbsp;using&nbsp;psize&nbsp;data<br>
&nbsp;<br>
Written&nbsp;by&nbsp;Todd&nbsp;Dolinsky&nbsp;based&nbsp;on&nbsp;original&nbsp;sed&nbsp;script&nbsp;by&nbsp;Nathan&nbsp;Baker<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;----------------------------<br>
&nbsp;<br>
PDB2PQR&nbsp;--&nbsp;An&nbsp;automated&nbsp;pipeline&nbsp;for&nbsp;the&nbsp;setup,&nbsp;execution,&nbsp;and&nbsp;analysis&nbsp;of<br>
Poisson-Boltzmann&nbsp;electrostatics&nbsp;calculations<br>
&nbsp;<br>
Copyright&nbsp;(c)&nbsp;2002-2011,&nbsp;Jens&nbsp;Erik&nbsp;Nielsen,&nbsp;University&nbsp;College&nbsp;Dublin;&nbsp;<br>
Nathan&nbsp;A.&nbsp;Baker,&nbsp;Battelle&nbsp;Memorial&nbsp;Institute,&nbsp;Developed&nbsp;at&nbsp;the&nbsp;Pacific&nbsp;<br>
Northwest&nbsp;National&nbsp;Laboratory,&nbsp;operated&nbsp;by&nbsp;Battelle&nbsp;Memorial&nbsp;Institute,&nbsp;<br>
Pacific&nbsp;Northwest&nbsp;Division&nbsp;for&nbsp;the&nbsp;U.S.&nbsp;Department&nbsp;Energy.;&nbsp;<br>
Paul&nbsp;Czodrowski&nbsp;&amp;&nbsp;Gerhard&nbsp;Klebe,&nbsp;University&nbsp;of&nbsp;Marburg.<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;All&nbsp;rights&nbsp;reserved.<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;Redistribution&nbsp;and&nbsp;use&nbsp;in&nbsp;source&nbsp;and&nbsp;binary&nbsp;forms,&nbsp;with&nbsp;or&nbsp;without&nbsp;modification,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;are&nbsp;permitted&nbsp;provided&nbsp;that&nbsp;the&nbsp;following&nbsp;conditions&nbsp;are&nbsp;met:<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*&nbsp;Redistributions&nbsp;of&nbsp;source&nbsp;code&nbsp;must&nbsp;retain&nbsp;the&nbsp;above&nbsp;copyright&nbsp;notice,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;this&nbsp;list&nbsp;of&nbsp;conditions&nbsp;and&nbsp;the&nbsp;following&nbsp;disclaimer.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*&nbsp;Redistributions&nbsp;in&nbsp;binary&nbsp;form&nbsp;must&nbsp;reproduce&nbsp;the&nbsp;above&nbsp;copyright&nbsp;notice,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;this&nbsp;list&nbsp;of&nbsp;conditions&nbsp;and&nbsp;the&nbsp;following&nbsp;disclaimer&nbsp;in&nbsp;the&nbsp;documentation&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;and/or&nbsp;other&nbsp;materials&nbsp;provided&nbsp;with&nbsp;the&nbsp;distribution.<br>
&nbsp;&nbsp;&nbsp;&nbsp;*&nbsp;Neither&nbsp;the&nbsp;names&nbsp;of&nbsp;University&nbsp;College&nbsp;Dublin,&nbsp;Battelle&nbsp;Memorial&nbsp;Institute,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pacific&nbsp;Northwest&nbsp;National&nbsp;Laboratory,&nbsp;US&nbsp;Department&nbsp;of&nbsp;Energy,&nbsp;or&nbsp;University<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;of&nbsp;Marburg&nbsp;nor&nbsp;the&nbsp;names&nbsp;of&nbsp;its&nbsp;contributors&nbsp;may&nbsp;be&nbsp;used&nbsp;to&nbsp;endorse&nbsp;or&nbsp;promote<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;products&nbsp;derived&nbsp;from&nbsp;this&nbsp;software&nbsp;without&nbsp;specific&nbsp;prior&nbsp;written&nbsp;permission.<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;THIS&nbsp;SOFTWARE&nbsp;IS&nbsp;PROVIDED&nbsp;BY&nbsp;THE&nbsp;COPYRIGHT&nbsp;HOLDERS&nbsp;AND&nbsp;CONTRIBUTORS&nbsp;"AS&nbsp;IS"&nbsp;AND&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;ANY&nbsp;EXPRESS&nbsp;OR&nbsp;IMPLIED&nbsp;WARRANTIES,&nbsp;INCLUDING,&nbsp;BUT&nbsp;NOT&nbsp;LIMITED&nbsp;TO,&nbsp;THE&nbsp;IMPLIED&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;WARRANTIES&nbsp;OF&nbsp;MERCHANTABILITY&nbsp;AND&nbsp;FITNESS&nbsp;FOR&nbsp;A&nbsp;PARTICULAR&nbsp;PURPOSE&nbsp;ARE&nbsp;DISCLAIMED.&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;IN&nbsp;NO&nbsp;EVENT&nbsp;SHALL&nbsp;THE&nbsp;COPYRIGHT&nbsp;OWNER&nbsp;OR&nbsp;CONTRIBUTORS&nbsp;BE&nbsp;LIABLE&nbsp;FOR&nbsp;ANY&nbsp;DIRECT,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;INDIRECT,&nbsp;INCIDENTAL,&nbsp;SPECIAL,&nbsp;EXEMPLARY,&nbsp;OR&nbsp;CONSEQUENTIAL&nbsp;DAMAGES&nbsp;(INCLUDING,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;BUT&nbsp;NOT&nbsp;LIMITED&nbsp;TO,&nbsp;PROCUREMENT&nbsp;OF&nbsp;SUBSTITUTE&nbsp;GOODS&nbsp;OR&nbsp;SERVICES;&nbsp;LOSS&nbsp;OF&nbsp;USE,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;DATA,&nbsp;OR&nbsp;PROFITS;&nbsp;OR&nbsp;BUSINESS&nbsp;INTERRUPTION)&nbsp;HOWEVER&nbsp;CAUSED&nbsp;AND&nbsp;ON&nbsp;ANY&nbsp;THEORY&nbsp;OF&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;LIABILITY,&nbsp;WHETHER&nbsp;IN&nbsp;CONTRACT,&nbsp;STRICT&nbsp;LIABILITY,&nbsp;OR&nbsp;TORT&nbsp;(INCLUDING&nbsp;NEGLIGENCE&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;OR&nbsp;OTHERWISE)&nbsp;ARISING&nbsp;IN&nbsp;ANY&nbsp;WAY&nbsp;OUT&nbsp;OF&nbsp;THE&nbsp;USE&nbsp;OF&nbsp;THIS&nbsp;SOFTWARE,&nbsp;EVEN&nbsp;IF&nbsp;ADVISED&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;OF&nbsp;THE&nbsp;POSSIBILITY&nbsp;OF&nbsp;SUCH&nbsp;DAMAGE.<br>
&nbsp;<br>
----------------------------</tt></p>
<p>
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<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Modules</strong></big></font></td></tr>
    
<tr><td bgcolor="#aa55cc"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><table width="100%" summary="list"><tr><td width="25%" valign=top><a href="pickle.html">pickle</a><br>
</td><td width="25%" valign=top><a href="src.psize.html">src.psize</a><br>
</td><td width="25%" valign=top><a href="string.html">string</a><br>
</td><td width="25%" valign=top><a href="sys.html">sys</a><br>
</td></tr></table></td></tr></table><p>
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<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Classes</strong></big></font></td></tr>
    
<tr><td bgcolor="#ee77aa"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><dl>
<dt><font face="helvetica, arial"><a href="src.inputgen.html#Elec">Elec</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.inputgen.html#Input">Input</a>
</font></dt></dl>
 <p>
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<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="Elec">class <strong>Elec</strong></a></font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>An&nbsp;object&nbsp;for&nbsp;the&nbsp;ELEC&nbsp;section&nbsp;of&nbsp;an&nbsp;APBS&nbsp;input&nbsp;file<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Elec-__init__"><strong>__init__</strong></a>(self, pqrpath, size, method, asyncflag, istrng<font color="#909090">=0</font>, potdx<font color="#909090">=0</font>)</dt><dd><tt>Initialize&nbsp;the&nbsp;variables&nbsp;that&nbsp;can&nbsp;be&nbsp;set&nbsp;in&nbsp;this&nbsp;object<br>
Users&nbsp;can&nbsp;modify&nbsp;any&nbsp;of&nbsp;these&nbsp;variables&nbsp;(that's&nbsp;why<br>
they're&nbsp;here!)</tt></dd></dl>

<dl><dt><a name="Elec-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Return&nbsp;the&nbsp;elec&nbsp;statement&nbsp;as&nbsp;a&nbsp;string.&nbsp;Check&nbsp;the&nbsp;method<br>
to&nbsp;see&nbsp;which&nbsp;keywords&nbsp;to&nbsp;use.</tt></dd></dl>

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<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="Input">class <strong>Input</strong></a></font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>The&nbsp;input&nbsp;class.&nbsp;&nbsp;Each&nbsp;input&nbsp;object&nbsp;is&nbsp;one&nbsp;APBS&nbsp;input&nbsp;file.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Input-__init__"><strong>__init__</strong></a>(self, pqrpath, size, method, asyncflag, istrng<font color="#909090">=0</font>, potdx<font color="#909090">=0</font>)</dt><dd><tt>Initialize&nbsp;the&nbsp;input&nbsp;file&nbsp;class.&nbsp;&nbsp;Each&nbsp;input&nbsp;file&nbsp;contains<br>
a&nbsp;PQR&nbsp;name,&nbsp;a&nbsp;list&nbsp;of&nbsp;elec&nbsp;objects,&nbsp;and&nbsp;a&nbsp;list&nbsp;of&nbsp;strings<br>
containing&nbsp;print&nbsp;statements.&nbsp;&nbsp;For&nbsp;starters&nbsp;assume&nbsp;two<br>
ELEC&nbsp;statements&nbsp;are&nbsp;needed,&nbsp;one&nbsp;for&nbsp;the&nbsp;inhomgenous&nbsp;and<br>
the&nbsp;other&nbsp;for&nbsp;the&nbsp;homogenous&nbsp;dielectric&nbsp;calculations.<br>
&nbsp;<br>
Users&nbsp;can&nbsp;edit&nbsp;the&nbsp;elec&nbsp;statements&nbsp;and&nbsp;the&nbsp;print&nbsp;statements.<br>
&nbsp;<br>
This&nbsp;assumes&nbsp;you&nbsp;have&nbsp;already&nbsp;run&nbsp;psize,&nbsp;either&nbsp;by<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;size.runPsize(/path/to/pqr)&nbsp;or<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;size.parseString(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;size.setAll()<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;pqrpath:&nbsp;&nbsp;&nbsp;The&nbsp;path&nbsp;to&nbsp;the&nbsp;PQR&nbsp;file&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;size:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;Psize&nbsp;object&nbsp;(psize)<br>
&nbsp;&nbsp;&nbsp;&nbsp;method:&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;method&nbsp;(para,&nbsp;auto,&nbsp;manual,&nbsp;async)&nbsp;to&nbsp;use<br>
&nbsp;&nbsp;&nbsp;&nbsp;asyncflag:&nbsp;1&nbsp;if&nbsp;async&nbsp;is&nbsp;desired,&nbsp;0&nbsp;otherwise</tt></dd></dl>

<dl><dt><a name="Input-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Return&nbsp;the&nbsp;text&nbsp;of&nbsp;the&nbsp;input&nbsp;file</tt></dd></dl>

<dl><dt><a name="Input-dumpPickle"><strong>dumpPickle</strong></a>(self)</dt><dd><tt>Make&nbsp;a&nbsp;Python&nbsp;pickle&nbsp;associated&nbsp;with&nbsp;the&nbsp;APBS&nbsp;input&nbsp;parameters</tt></dd></dl>

<dl><dt><a name="Input-printInputFiles"><strong>printInputFiles</strong></a>(self)</dt><dd><tt>Make&nbsp;the&nbsp;input&nbsp;file(s)&nbsp;associated&nbsp;with&nbsp;this&nbsp;object</tt></dd></dl>

</td></tr></table></td></tr></table><p>
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<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Functions</strong></big></font></td></tr>
    
<tr><td bgcolor="#eeaa77"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><dl><dt><a name="-main"><strong>main</strong></a>()</dt></dl>
 <dl><dt><a name="-splitInput"><strong>splitInput</strong></a>(filename)</dt><dd><tt>Split&nbsp;the&nbsp;parallel&nbsp;input&nbsp;file&nbsp;into&nbsp;multiple&nbsp;async&nbsp;file&nbsp;names<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;filename:&nbsp;&nbsp;The&nbsp;path&nbsp;to&nbsp;the&nbsp;original&nbsp;parallel&nbsp;input<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;file&nbsp;(string)</tt></dd></dl>
 <dl><dt><a name="-usage"><strong>usage</strong></a>()</dt><dd><tt>Display&nbsp;the&nbsp;usage&nbsp;information&nbsp;for&nbsp;this&nbsp;script</tt></dd></dl>
</td></tr></table><p>
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<tr bgcolor="#55aa55">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Data</strong></big></font></td></tr>
    
<tr><td bgcolor="#55aa55"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><strong>__author__</strong> = 'Todd Dolinsky, Nathan Baker, Yong Huang'<br>
<strong>__date__</strong> = '21 April 2007'</td></tr></table><p>
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<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Author</strong></big></font></td></tr>
    
<tr><td bgcolor="#7799ee"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%">Todd&nbsp;Dolinsky,&nbsp;Nathan&nbsp;Baker,&nbsp;Yong&nbsp;Huang</td></tr></table>
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